
CPPTRAJ: Trajectory Analysis. V5.1.0
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| Date/time: 02/25/23 11:08:04
| Available memory: 959.607 MB

	Reading 'COM.prmtop' as Amber Topology
	CHAMBER topology:
                                 CHARMM force field: No FF information parsed...
	Radius Set: H(N)-modified Bondi radii (mbondi2)
INPUT: Reading input from 'STDIN'
  [trajin COM_traj_0.xtc 10 9610 1600]
	Reading 'COM_traj_0.xtc' as Gromacs XTC
Warning: Trajectory box type is 'Triclinic' but topology box type is 'None'.
Warning: Setting topology box information from trajectory.
  [noprogress]
	Progress bar will not be used during Run.
  [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first]
    RMSD: (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), reference is first frame (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), mass-weighted.
	Best-fit RMSD will be calculated, coords will be rotated and translated.
  [outtraj _GMXMMPBSA_complex.pdb onlyframes 1 nobox pdb]
	Saving frames 1
	Writing '_GMXMMPBSA_complex.pdb' as PDB
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [outtraj _GMXMMPBSA_dummycomplex.inpcrd onlyframes 1 nobox restart]
	Saving frames 1
	Writing '_GMXMMPBSA_dummycomplex.inpcrd' as Amber Restart
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [outtraj _GMXMMPBSA_complex.mdcrd.0 onlyframes 1-8 nobox]
Warning: Format not specified and extension '.0' not recognized. Defaulting to Amber Trajectory.
	Saving frames 1 2 3 4 5 6 7 8
	Writing '_GMXMMPBSA_complex.mdcrd.0' as Amber Trajectory
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [strip :437-480]
    STRIP: Stripping atoms in mask [:437-480]
  [outtraj _GMXMMPBSA_receptor.pdb onlyframes 1 nobox pdb]
	Saving frames 1
	Writing '_GMXMMPBSA_receptor.pdb' as PDB
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [outtraj _GMXMMPBSA_dummyreceptor.inpcrd onlyframes 1 nobox restart]
	Saving frames 1
	Writing '_GMXMMPBSA_dummyreceptor.inpcrd' as Amber Restart
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [outtraj _GMXMMPBSA_receptor.mdcrd.0 onlyframes 1-8 nobox]
Warning: Format not specified and extension '.0' not recognized. Defaulting to Amber Trajectory.
	Saving frames 1 2 3 4 5 6 7 8
	Writing '_GMXMMPBSA_receptor.mdcrd.0' as Amber Trajectory
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [unstrip]
  [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first]
    RMSD: (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), reference is first frame (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), mass-weighted.
	Best-fit RMSD will be calculated, coords will be rotated and translated.
  [strip :1-436]
    STRIP: Stripping atoms in mask [:1-436]
  [outtraj _GMXMMPBSA_ligand.pdb onlyframes 1 nobox pdb]
	Saving frames 1
	Writing '_GMXMMPBSA_ligand.pdb' as PDB
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [outtraj _GMXMMPBSA_dummyligand.inpcrd onlyframes 1 nobox restart]
	Saving frames 1
	Writing '_GMXMMPBSA_dummyligand.inpcrd' as Amber Restart
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [outtraj _GMXMMPBSA_ligand.mdcrd.0 onlyframes 1-8 nobox]
Warning: Format not specified and extension '.0' not recognized. Defaulting to Amber Trajectory.
	Saving frames 1 2 3 4 5 6 7 8
	Writing '_GMXMMPBSA_ligand.mdcrd.0' as Amber Trajectory
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'
  [unstrip]
  [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first]
    RMSD: (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), reference is first frame (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), mass-weighted.
	Best-fit RMSD will be calculated, coords will be rotated and translated.
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):
 0: COM.prmtop, 7012 atoms, 480 res, box: Triclinic, 3 mol

INPUT TRAJECTORIES (1 total):
 0: 'COM_traj_0.xtc' is a GROMACS XTC file, Parm COM.prmtop (Triclinic box) (reading 7 of 10001)
  Coordinate processing will occur on 7 frames.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'COM.prmtop' (16 actions):
  0: [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first]
	Target mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](7012)
	Reference topology: COM.prmtop
	Reference mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](7012)
  1: [outtraj _GMXMMPBSA_complex.pdb onlyframes 1 nobox pdb]
        '_GMXMMPBSA_complex.pdb' is a PDB file, Parm COM.prmtop no box info,: Writing frames 1
	Has coordinates, time
  2: [outtraj _GMXMMPBSA_dummycomplex.inpcrd onlyframes 1 nobox restart]
        '_GMXMMPBSA_dummycomplex.inpcrd' is an AMBER restart file, Parm COM.prmtop no box info,: Writing frames 1
	Has coordinates, time
  3: [outtraj _GMXMMPBSA_complex.mdcrd.0 onlyframes 1-8 nobox]
        '_GMXMMPBSA_complex.mdcrd.0' is an AMBER trajectory, Parm COM.prmtop no box info,: Writing frames 1 2 3 4 5 6 7 8
	Has coordinates, time
  4: [strip :437-480]
	Stripping 505 atoms.
	Stripped topology: 6507 atoms, 436 res, box: Triclinic, 2 mol
  5: [outtraj _GMXMMPBSA_receptor.pdb onlyframes 1 nobox pdb]
        '_GMXMMPBSA_receptor.pdb' is a PDB file, Parm COM.prmtop no box info,: Writing frames 1
	Has coordinates, time
  6: [outtraj _GMXMMPBSA_dummyreceptor.inpcrd onlyframes 1 nobox restart]
        '_GMXMMPBSA_dummyreceptor.inpcrd' is an AMBER restart file, Parm COM.prmtop no box info,: Writing frames 1
	Has coordinates, time
  7: [outtraj _GMXMMPBSA_receptor.mdcrd.0 onlyframes 1-8 nobox]
        '_GMXMMPBSA_receptor.mdcrd.0' is an AMBER trajectory, Parm COM.prmtop no box info,: Writing frames 1 2 3 4 5 6 7 8
	Has coordinates, time
  8: [unstrip]
  9: [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first]
	Target mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](7012)
	Reference topology: COM.prmtop
	Reference mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](7012)
  10: [strip :1-436]
	Stripping 6507 atoms.
	Stripped topology: 505 atoms, 44 res, box: Triclinic, 1 mol
  11: [outtraj _GMXMMPBSA_ligand.pdb onlyframes 1 nobox pdb]
        '_GMXMMPBSA_ligand.pdb' is a PDB file, Parm COM.prmtop no box info,: Writing frames 1
	Has coordinates, time
  12: [outtraj _GMXMMPBSA_dummyligand.inpcrd onlyframes 1 nobox restart]
        '_GMXMMPBSA_dummyligand.inpcrd' is an AMBER restart file, Parm COM.prmtop no box info,: Writing frames 1
	Has coordinates, time
  13: [outtraj _GMXMMPBSA_ligand.mdcrd.0 onlyframes 1-8 nobox]
        '_GMXMMPBSA_ligand.mdcrd.0' is an AMBER trajectory, Parm COM.prmtop no box info,: Writing frames 1 2 3 4 5 6 7 8
	Has coordinates, time
  14: [unstrip]
  15: [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first]
	Target mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](7012)
	Reference topology: COM.prmtop
	Reference mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](7012)
----- COM_traj_0.xtc (10-9610, 1600) -----

Read 7 frames and processed 7 frames.
TIME: Avg. throughput= 79.0719 frames / second.

ACTION OUTPUT:
    OUTTRAJ: '_GMXMMPBSA_complex.pdb': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_dummycomplex.inpcrd': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.0': Wrote 7 frames.
    OUTTRAJ: '_GMXMMPBSA_receptor.pdb': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_dummyreceptor.inpcrd': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_receptor.mdcrd.0': Wrote 7 frames.
    OUTTRAJ: '_GMXMMPBSA_ligand.pdb': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_dummyligand.inpcrd': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_ligand.mdcrd.0': Wrote 7 frames.
TIME: Analyses took 0.0000 seconds.

DATASETS (3 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 7 (0.056 kB)
	RMSD_00002 "RMSD_00002" (double, rms), size is 7 (0.056 kB)
	RMSD_00003 "RMSD_00003" (double, rms), size is 7 (0.056 kB)
    Total data set memory usage is at least 0.168 kB

RUN TIMING:
TIME:		Init               : 0.0001 s (  0.06%)
TIME:		Trajectory Process : 0.0885 s ( 99.62%)
TIME:		Action Post        : 0.0000 s (  0.01%)
TIME:		Analysis           : 0.0000 s (  0.00%)
TIME:		Data File Write    : 0.0000 s (  0.01%)
TIME:		Other              : 0.0003 s (  0.00%)
TIME:	Run Total 0.0889 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 0.1891 seconds.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
  Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
  Theory Comput., 2013, 9 (7), pp 3084-3095.

